Sometimes yes, but sometimes it is good to have the good light gathering with a large Aperture without having to have the very shallow DoF.

This is a profound misunderstanding that many have, which causes a great deal of confusion. First of all, we need to distinguish between the relative aperture (f-ratio) and the virtual aperture (entrance pupil), where the relative aperture is the quotient of the focal length and the diameter of the virtual aperture. For example, a 25mm lens with an 18mm aperture diameter will have a relative aperture of 25mm / 18mm = 1.4. Likewise, a 50mm lens with an 18mm aperture diameter will have a relative aperture of 50mm / 18mm = 2.8. Thus, 25mm f/1.4 and 50mm f/2.8 both have the same aperture diameter.

As it turns out, for a given perspective, framing, and display size of the photo, the same aperture diameter results in the same DOF. If we also include the same scene luminance and shutter speed, it also results in the same total amount of light falling on the sensor, which, in turn, will result in the same noise for equally efficient sensors.

So, if we took a photo of a scene at 25mm f/1.4 1/100 on mFT and 50mm f/2.8 1/100 on FF from the same position, and displayed the photos at the same size, they would have the same DOF and the same amount of light would fall on the mFT and FF sensors, resulting in the same noise if the sensors were equally efficient.

In other words, your statement that "sometimes it is good to have the good light gathering with a large Aperture without having to have the very shallow DoF" is a physical contradiction. Specifically, 25mm f/1.4 does not have a "larger aperture" than 50mm f/2.8 -- in fact, they are the same. Of course, f/1.4 is a lower f-ratio than f/2.8, but that is neither here nor there in terms of cross-format comparisons.

That would of course be perfectly true as long as MFT and FF sensors were equally efficient.

Yes. Sensor efficiency is the wild card.

Not a wild card. Just something to be taken into account.

It's just that (as you already know) they aren't, as exemplified below. The E-M1 is about 1.5 EV ahead of the A7R for DR (and thus shadow noise) at the same DoF.

But, as you know, DR considers only the read noise and disregards the photon noise,

That depends on the comparison at issue. In the present one, the implication is that the E-M1 will do about 1.5 EV better with regard to read noise (and thus shadow noise) whereas in the midtones and highlights, the difference will be significantly less.

which is the primary source of noise in most all photos,

While that's true, it has little implications for perceived IQ. What matters is SNR (the signal-to-noise ratio as opposed to noise in absolute terms), in particular the SNR where it is weakest and the shortcomings therefore most visible, i.e., in the shadows. And in that respect, it is the other way around.

and the greater read noise per area of FF sensors is a direct consequence of the greater pixel count.

I am afraid it's not that simple. First, let's have a look at the same graph when substituting the 16 MP Nikon Df and the 24 MP Sony A7 for the 36 MP Sony A7R.

First, although the A7 has significantly fewer pixels than the A7R, it doesn't do better relative to the E-M1 than the A7R does. Second, while the Df, with the same pixel count as the E-M1, does better than the A7/A7R at high ISOs, it a) doesn't bridge the gap fully at these ISOs (i.e. DR remains lower than that of the E-M1 at the same DoF), and b) does worse than the A7/A7R at lower ISOs.

So, if we instead compare, say, the EM1 at ISO 3200 to the Nikon Df at ISO 12800:

I mean, we can make any comparison we like (someone above compared the 8+ year old 5D to the EM1), and that is perfectly fine if you are considering a 5D vs an EM1.

Yes, we can make such a comparison. But that wasn't the one I was making. I was comparing current sensors.

Of course, if your photography will generally require you to shoot the larger format at the same DOF and shutter speed you would use with the smaller format, then you will almost invariably be better served with the smaller format, unless the larger format has some particular operational advantage that the smaller format does not offer.